From 95138f518bb8573b2b5024cbf4e8994bb8e5cc36 Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Sat, 11 Jan 2025 16:37:23 +0100
Subject: [PATCH] add statistical analysis assay and protocol

---
 assays/StatisticalAnalysis/README.md             |   0
 assays/StatisticalAnalysis/dataset/.gitkeep      |   0
 assays/StatisticalAnalysis/isa.assay.xlsx        | Bin 0 -> 6900 bytes
 assays/StatisticalAnalysis/protocols/.gitkeep    |   0
 .../protocols/StatisticalAnalysisProtocol.md     |   5 +++++
 5 files changed, 5 insertions(+)
 create mode 100644 assays/StatisticalAnalysis/README.md
 create mode 100644 assays/StatisticalAnalysis/dataset/.gitkeep
 create mode 100644 assays/StatisticalAnalysis/isa.assay.xlsx
 create mode 100644 assays/StatisticalAnalysis/protocols/.gitkeep
 create mode 100644 assays/StatisticalAnalysis/protocols/StatisticalAnalysisProtocol.md

diff --git a/assays/StatisticalAnalysis/README.md b/assays/StatisticalAnalysis/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/assays/StatisticalAnalysis/dataset/.gitkeep b/assays/StatisticalAnalysis/dataset/.gitkeep
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index 0000000..e69de29
diff --git a/assays/StatisticalAnalysis/isa.assay.xlsx b/assays/StatisticalAnalysis/isa.assay.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..e21b3e21066400d14f392eb8f7e6d6056cc472f5
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diff --git a/assays/StatisticalAnalysis/protocols/.gitkeep b/assays/StatisticalAnalysis/protocols/.gitkeep
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index 0000000..e69de29
diff --git a/assays/StatisticalAnalysis/protocols/StatisticalAnalysisProtocol.md b/assays/StatisticalAnalysis/protocols/StatisticalAnalysisProtocol.md
new file mode 100644
index 0000000..1cf7ca6
--- /dev/null
+++ b/assays/StatisticalAnalysis/protocols/StatisticalAnalysisProtocol.md
@@ -0,0 +1,5 @@
+## Statistical analysis
+
+Initial raw data from the qPCR and HPLC experiments were processed using Excel software (Microsoft Office 365). These processed data were used for statistical analysis. All experiments made use of 3–4 biological replicates for each accession. The accessions were grouped into low, medium, and high sulfate groups, which were then used in a one-way ANOVA. Furthermore, a Tukey honest significant difference (HSD) post-hoc between significantly different groups was performed. The level of significance was set at P≤0.05.
+
+For clustering analysis, we extracted ~400 genes, annotated in S, N, and phosphorus (P) homeostasis and metabolism (www.arabidopsis.org) from a previously published dataset (Kawakatsu et al., 2016), and transformed the counts into z-scores on a gene-by-gene basis in the seven accessions, three from our low S content group, three from our high S content group, and the reference accession, Col-0. Multiple Experiment Viewer software (TIGR; http://mev.tm4.org) was used to create heat maps and perform cluster analysis using QTC with Pearson correlation, hierarchical clustering: average linkage method, and diameter 0.1. The pair-wise correlation analysis between the traits was performed using the ‘Hmisc’ and ‘corrplot’ packages in R (https://www.Rproject.org). A multivariate network was created in Cytoscape (Su et al., 2014) based on significant pair-wise correlations between all quantified traits.
\ No newline at end of file
-- 
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